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Windows 7: Placement of the 'Program Files' folder(s)

I'm about to reinstall my windows and after that kind of reorganize everything..

So I have a SSD and a HDD. Windows (x64) will be on the SSD. Which means there will also be 'Program Files' and 'Program Files (x86)' on there.
Now on the HDD (only one partition there), I will manually make two more folders: 'Program Files' and 'Program Files (x86)'. My question is: do the 'Program Files' folders have to be in the root of the drive (e.x. H:/Program Files)? Because if not I would like them to be in a 'Programs' folder, which will be in the root, along with 'Media', 'Games' and 'Stuff'. (H:/Programs/Program Files)
Actually this is how I have it now, but I am wondering if it is ok or maybe not recommended..
What made me think of this is: I have the Origin client from EA, and when I open it it automatically creates a folder in the root of the HDD called 'Program Files (x86)'. There's an 'Origin' folder in it but its empty. I deleted it to see if it would recreate itself, and the next time I opened origin the 'Program Files (x86)' folder reappeared - even tried a few times to confirm.

So is Windows, or any programs, bothered by 'Program Files' not being in the root of a partition? Can I easily stick it into another folder? (of course before installing any programs in it).

I found this page where some people moved Program Files. But it didn't look trivial:Move Program Files

I'm wondering if perhaps you can install your programs to folders underneath program files then move that folder to another physical disk. Then make a hard link to it. That way Windows Registry settings all the rest should still point to the same place. In fact PC Magazine has a utility to do it. I think it costs $7 or $8. Also I've seen some people use other hard link utilities designed for moving games, for free. (In Linux when a partition started to fill up I just made a link to another and moved programs over. It worked quite easily there.)

If you try it I would make plenty of backup images to external drives so that you can get back to square one. But if it's a clean install you're starting with, that's the time to experiment. Also I'd look through Brink's Tutorials. Anything that refers to hard links or junction points.

I don't want to create links, and I don't want to move the 'Program Files' which is on the C/ drive. I just want to make things organized by creating 4 folders on my HDD partition, and one of these would be 'Programs' with 'Program files' inside it. I would make this from the start, I wouldn't move it anywhere. I'm just woundering if it is ok if 'Program Files' is not in the root of a drive. Because of the name or any other reason.

That program for linking, why don't you try it out? I never heard of it, but maybe there's a trial version.

But if from the beginning I have an empty H:/Programs/Program Files
And during installation I tell it to install into H:/Programs/Program Files
It will be installed there and it would look for its files in there, because I gave that location during installation.

I already did, in Linux dozens of times. Been there, done that. When you mentioned SSD I thought you were trying to move Program Files to make more room on the SSD. Most people with Windows on the SSD look for ways to minimize the Windows footprint on the drive.

But if from the beginning I have an empty H:/Programs/Program Files
And during installation I tell it to install into H:/Programs/Program Files
It will be installed there and it would look for its files in there, because I gave that location during installation.

Could even this be a problem?

I already gave my opinion. But they call 'em Personal Computers for a reason. If that's how you want to do it, go for it. It's your machine.

I already did, in Linux dozens of times. Been there, done that. When you mentioned SSD I thought you were trying to move Program Files to make more room on the SSD. Most people with Windows on the SSD look for ways to minimize the Windows footprint on the drive.

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